Contacts of the helix formed by residues 944 - 969 (chain G) in PDB entry 1SOJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 944 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678G ASN* 2.7 31.3 + - + +
943G LYS* 1.3 76.5 - - - +
945G ARG* 1.3 69.9 + - + +
946G ASP* 3.9 15.0 - - + +
947G LEU* 3.7 27.8 - - + +
948G HIS* 3.0 16.1 + - - +
1064G HIS* 3.4 21.2 - - + -
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Residues in contact with ARG 945 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943G LYS 3.7 0.6 + - - -
944G VAL* 1.3 78.3 - - + +
946G ASP* 1.3 65.4 + - - +
948G HIS* 3.2 1.7 + - + -
949G LEU* 2.9 46.9 + - + +
1064G HIS* 4.9 1.0 + - - -
1068G ASN* 3.8 22.6 + - - +
1071G ILE* 3.8 16.2 - - + -
915L ASN* 2.8 70.5 + - - +
916L GLY* 4.6 0.8 - - - +
918L GLU* 2.5 40.4 + - - +
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Residues in contact with ASP 946 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944G VAL* 3.9 15.3 - - + +
945G ARG* 1.3 80.3 - - - +
947G LEU* 1.3 76.0 + - - +
949G LEU* 3.7 5.1 + - - +
950G LYS* 3.4 19.6 + - - +
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Residues in contact with LEU 947 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678G ASN* 4.1 22.0 - - - +
679G PHE 3.7 23.3 - - - +
680G PRO* 4.9 9.9 - - + -
681G ILE* 5.4 2.0 - - + -
682G PHE* 4.8 16.2 - - + -
943G LYS* 4.0 33.0 - - + +
944G VAL* 3.2 14.8 + - + +
945G ARG 3.2 0.4 - - - -
946G ASP* 1.3 92.3 - - - +
948G HIS* 1.3 68.1 + - - +
950G LYS* 3.0 16.4 + - - +
951G TRP* 3.0 29.5 + - + +
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Residues in contact with HIS 948 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940G GLY* 3.5 17.1 + - - +
941G PRO* 3.3 43.2 - - + +
944G VAL 3.0 16.4 + - - +
945G ARG* 3.6 4.3 - - - +
947G LEU* 1.3 78.3 - - - +
949G LEU* 1.3 61.9 + - + +
951G TRP* 3.3 4.9 + - - +
952G THR* 2.8 48.3 + - - -
988G GLN* 3.6 11.4 - - - -
992G ILE* 5.2 0.9 - - + -
1068G ASN* 3.7 26.4 - - - +
1071G ILE* 4.6 1.8 - - + -
1072G TRP* 2.9 36.8 + + - -
2117G IBM 4.7 1.5 + - - -
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Residues in contact with LEU 949 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945G ARG* 2.9 45.2 + - + +
946G ASP* 4.1 4.7 - - - +
948G HIS* 1.3 71.7 - - + +
950G LYS* 1.3 66.9 + - - +
952G THR* 3.3 3.7 + - - +
953G GLU* 2.9 25.3 + - - +
1071G ILE* 4.1 7.4 - - + -
1072G TRP* 3.6 36.3 - - + -
918L GLU* 3.2 30.5 - - + +
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Residues in contact with LYS 950 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682G PHE* 3.5 49.8 - - + -
946G ASP* 3.4 13.1 + - - +
947G LEU* 3.0 10.6 + - - +
949G LEU* 1.3 80.1 - - - +
951G TRP* 1.3 64.3 + - - +
953G GLU* 3.4 28.4 + - - +
954G GLY* 3.3 12.8 + - - -
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Residues in contact with TRP 951 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681G ILE* 4.2 8.4 - - + +
682G PHE* 3.6 37.0 - + - -
736G TYR* 3.6 38.1 - + + +
738G ASN* 5.1 3.1 - - - -
740G ILE* 3.8 15.0 - - + -
741G HIS* 3.8 32.8 - - + -
744G ASP* 3.3 36.7 + - + -
939G ASN* 5.4 1.6 - - - -
940G GLY* 4.7 21.1 - - - -
943G LYS* 5.0 4.3 - - + +
947G LEU* 3.0 35.6 + - + +
948G HIS* 3.8 6.5 - - - +
950G LYS* 1.3 75.4 - - - +
952G THR* 1.3 66.6 + - - +
954G GLY* 2.8 14.6 + - - -
955G ILE* 3.0 19.8 + - + +
2117G IBM 5.7 0.4 - - - -
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Residues in contact with THR 952 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948G HIS* 2.8 33.4 + - - -
949G LEU* 3.5 9.1 - - + -
951G TRP* 1.3 75.2 - - - +
953G GLU* 1.3 64.5 + - - +
955G ILE* 3.2 13.9 + - + +
956G VAL* 3.0 27.1 + - + +
984G LEU* 3.7 24.5 - - + -
988G GLN* 2.8 40.2 + - + +
1072G TRP* 4.4 8.4 - - + -
2117G IBM 4.6 0.5 + - - -
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Residues in contact with GLU 953 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949G LEU 2.9 12.6 + - - +
950G LYS* 3.4 40.0 + - - +
952G THR* 1.3 77.0 - - - +
954G GLY* 1.3 58.9 + - - +
956G VAL* 3.1 9.4 - - + +
957G ASN* 2.6 49.2 + - - +
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Residues in contact with GLY 954 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G PRO* 3.6 24.0 - - - +
736G TYR* 3.7 9.1 - - - +
950G LYS 3.3 6.0 + - - -
951G TRP* 2.8 16.2 + - - -
953G GLU* 1.3 73.7 + - - +
955G ILE* 1.3 62.8 + - - -
957G ASN* 3.3 5.8 + - - -
958G GLU* 3.1 23.2 + - - +
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Residues in contact with ILE 955 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736G TYR* 3.4 41.5 - - + +
951G TRP* 3.0 29.8 + - + +
952G THR* 3.2 8.3 + - + +
954G GLY* 1.3 73.5 - - - +
956G VAL* 1.3 61.9 + - + +
958G GLU* 3.2 5.6 + - - +
959G PHE* 2.9 57.8 + - + -
988G GLN* 5.2 0.2 - - - +
2117G IBM 3.6 53.4 - - + +
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Residues in contact with VAL 956 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952G THR* 3.0 13.6 + - + +
953G GLU* 3.1 19.7 - - + +
955G ILE* 1.3 77.2 - - + +
957G ASN* 1.3 66.5 + - - +
959G PHE* 3.0 8.5 + - + +
960G TYR* 2.7 63.1 + - + +
976G PHE 5.5 0.4 - - - +
984G LEU* 3.6 32.8 - - + -
987G LEU* 3.9 22.7 - - + -
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Residues in contact with ASN 957 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G PRO* 4.0 14.0 - - + +
953G GLU* 2.6 47.0 + - - +
954G GLY* 3.7 6.4 - - - +
955G ILE 3.3 0.4 - - - -
956G VAL* 1.3 79.8 - - - +
958G GLU* 1.3 62.9 + - - +
960G TYR* 3.4 14.4 + - - +
961G GLU* 3.1 26.9 + - - +
979G ARG* 4.7 7.1 + - - +
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Residues in contact with GLU 958 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734G ILE* 3.8 6.4 - - + +
735G PRO* 3.4 19.9 - - + +
736G TYR* 2.8 30.5 + - + -
737G HIS* 2.6 42.5 + - - -
825G HIS* 4.4 0.2 + - - -
827G GLY* 3.3 35.4 - - - +
954G GLY 3.1 8.9 + - - +
955G ILE* 3.4 9.4 - - - +
956G VAL 3.1 0.2 - - - -
957G ASN* 1.3 75.6 - - - +
959G PHE* 1.3 70.6 + - + +
961G GLU* 3.1 10.5 + - - +
962G GLN* 3.1 19.9 + - - +
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Residues in contact with PHE 959 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737G HIS* 6.0 2.7 - - - -
829G THR* 4.5 13.2 - - + -
955G ILE* 2.9 41.0 + - + -
956G VAL* 3.5 10.8 - - - +
958G GLU* 1.3 80.8 - - + +
960G TYR* 1.3 58.0 + - + +
962G GLN* 3.1 8.0 + - - +
963G GLY 2.8 23.6 + - - -
975G PRO 5.8 0.2 - - - -
976G PHE* 4.4 8.5 - - + +
977G MET* 3.5 54.3 - - + +
987G LEU* 4.1 29.8 - - + -
2117G IBM 4.0 29.4 - + + -
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Residues in contact with TYR 960 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956G VAL* 2.7 52.4 + - + +
957G ASN* 3.8 9.6 - - - +
959G PHE* 1.3 73.6 - - + +
961G GLU* 1.3 58.2 + - - +
963G GLY* 3.1 1.0 + - - -
964G ASP* 2.9 34.3 + - - +
976G PHE 3.4 21.9 + - - -
977G MET* 3.4 23.0 - - - +
978G ASP 4.1 3.6 - - - -
979G ARG* 3.4 56.1 - - + +
982G PRO* 3.5 23.9 - - + +
983G GLN 4.8 0.2 + - - -
984G LEU* 4.7 11.4 + - - +
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Residues in contact with GLU 961 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734G ILE* 5.3 4.0 - - - +
735G PRO* 3.7 28.0 - - - +
828G ARG* 3.8 18.4 + - - +
957G ASN* 3.1 16.5 + - - +
958G GLU* 3.1 10.0 + - - +
960G TYR* 1.3 74.9 - - - +
962G GLN* 1.3 65.8 + - - +
964G ASP* 3.2 7.9 + - - +
965G GLU* 3.1 19.8 + - - +
979G ARG* 4.4 9.2 - - - +
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Residues in contact with GLN 962 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827G GLY 4.4 1.3 - - - +
828G ARG* 3.6 25.8 - - + +
829G THR* 3.1 46.0 + - - +
832G PHE* 3.6 26.6 - - + +
958G GLU 3.1 12.3 + - - +
959G PHE* 3.1 10.3 + - - +
961G GLU* 1.3 77.4 - - - +
963G GLY* 1.3 57.9 + - - +
965G GLU* 3.2 2.9 + - - +
966G GLU* 3.0 47.8 + - - +
974G SER* 3.9 3.6 + - - -
977G MET* 3.4 22.1 - - - +
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Residues in contact with GLY 963 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778F ARG* 4.7 0.2 - - - -
959G PHE 2.8 10.7 + - - -
960G TYR 3.1 0.4 + - - -
961G GLU 3.0 0.4 - - - -
962G GLN* 1.3 75.1 - - - +
964G ASP* 1.3 65.8 + - - +
966G GLU* 3.2 16.0 + - - +
967G ALA* 2.9 23.4 + - - +
973G ILE* 3.9 13.0 - - - +
977G MET* 3.5 23.6 - - - -
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Residues in contact with ASP 964 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776F ASP* 4.2 2.4 - - - +
777F GLY* 3.8 26.2 - - - +
778F ARG* 2.8 46.1 + - + +
960G TYR 2.9 12.5 + - - +
961G GLU* 3.2 9.4 + - - +
963G GLY* 1.3 75.6 - - - +
965G GLU* 1.3 56.8 + - - +
967G ALA* 3.2 3.8 - - - +
968G ASN* 2.9 32.5 + - - -
979G ARG* 2.5 34.1 + - - -
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Residues in contact with GLU 965 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872F LEU* 4.9 2.9 - - - +
873F HIS* 3.4 30.6 + - + +
828G ARG* 2.7 35.6 + - - +
832G PHE* 3.6 21.0 - - + -
961G GLU 3.1 7.1 + - - +
962G GLN 3.6 7.4 - - - +
963G GLY 3.1 0.8 - - - -
964G ASP* 1.3 74.3 - - - +
966G GLU* 1.3 68.5 + - - +
967G ALA 3.0 1.1 - - - -
968G ASN* 2.9 10.7 + - - +
969G LEU* 2.8 39.8 + - - +
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Residues in contact with GLU 966 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832G PHE* 3.7 21.1 - - + +
962G GLN* 3.0 29.7 + - - +
963G GLY* 3.6 15.6 + - - +
965G GLU* 1.3 74.7 - - - +
967G ALA* 1.3 59.4 + - - +
969G LEU* 3.1 8.8 + - - -
970G GLY 3.1 3.3 + - - -
971G LEU* 2.7 43.3 + - + +
972G PRO 4.1 15.4 - - - +
973G ILE* 3.5 5.3 - - - +
974G SER* 2.6 48.4 + - - -
977G MET* 4.5 0.7 - - - +
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Residues in contact with ALA 967 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778F ARG* 4.1 20.2 - - + +
963G GLY 2.9 13.0 + - - +
964G ASP* 3.2 13.7 - - - +
966G GLU* 1.3 76.7 - - - +
968G ASN* 1.3 57.1 + - - +
970G GLY* 2.6 29.6 + - - -
971G LEU 4.3 6.0 + - - -
973G ILE* 4.2 14.5 - - + +
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Residues in contact with ASN 968 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714F LYS* 4.4 12.1 - - - +
777F GLY 3.1 23.4 + - - -
778F ARG* 3.6 5.1 - - - +
779F ILE* 3.1 36.7 + - + +
781F HIS* 5.1 10.1 + - - -
872F LEU 4.3 0.7 - - - +
873F HIS* 3.8 40.9 + - + +
964G ASP 2.9 19.6 + - - +
965G GLU* 2.9 16.9 + - - +
967G ALA* 1.3 71.9 - - - +
969G LEU* 1.3 58.5 + - - +
970G GLY 3.1 1.2 + - - -
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Residues in contact with LEU 969 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872F LEU* 3.6 25.6 - - + +
873F HIS* 3.4 27.4 - - + +
832G PHE* 3.9 22.2 - - + -
836G THR* 4.1 9.0 - - + -
965G GLU* 2.8 36.2 + - - +
966G GLU 3.6 4.9 - - - +
967G ALA 3.0 0.4 + - - -
968G ASN* 1.3 72.9 - - - +
970G GLY* 1.3 62.4 + - - +
971G LEU* 3.4 32.0 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il